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Ardem Patapoutian @ardemp.bskyverified.social · Apr 9

Published an op-ed for @cnn.com: “Nobel laureate: I owe America my success. Today, its scientific future is in danger.”
A personal reflection on what’s at stake as science funding gets slashed. I’d be grateful if you could amplify both in and beyond the science world.
www.cnn.com/2025/04/09/h...

Nobel laureate: I owe America my success. Today, its scientific future is in danger | CNN

Dr. Ardem Patapoutian says he watches “with deep sadness as the United States’ remarkable scientific enterprise, which took generations of hard work and national investment to build, faces a concerted...

www.cnn.com

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Alex Kwan @alexkwan.bsky.social · Apr 9

A much-needed joint effort from five labs to see which behavioral effects of psilocybin in mice are reliable, and which may be spurious 🐁🍄

@theborislab.bsky.social @mazenkheirbek.bsky.social @indigenerd.bsky.social Vikaas Sohal and Stephan Lammel 👏

www.biorxiv.org/content/10.1...

A multi-institutional investigation of psilocybin's effects on mouse behavior

Studies reporting novel therapeutic effects of psychedelic drugs are rapidly emerging. However, the reproducibility and reliability of these findings could remain uncertain for years. Here, we impleme...

www.biorxiv.org

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Justin English @justingenglish.bsky.social · Apr 9

Yeah, this was a real headache, and was the impetus for writing the pairwise program. Alignment success rates also varied based on chemistry (see v9 vs. v10 in supplement). Maybe because some of our reads were shorter than medaka was intended for?

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Kristian G. Andersen @kgandersen.bsky.social · Apr 9

Very thankful to @sandiegouniontribune.com for covering the termination of our wastewater surveillance in San Diego.

If we don't want to lose sight of infectious diseases in our community, we need new funding - please reach out: searchcovid.info

www.sandiegouniontribune.com/2025/04/07/d...

DOGE cuts shut down San Diego County’s wastewater testing system

Other alternatives are available, but none show coronavirus subtypes like San Diego’s SEARCH

www.sandiegouniontribune.com

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Justin English @justingenglish.bsky.social · Apr 8

We are satisfied with the results and will use this pipeline until such a time that 100% accurate single molecule Nanopore is achieved. We are now using this in many of our synthetic biology pipelines -- directed evolution, MPRAs, DMS libraries. Hit me up with questions or for help.

Justin English @justingenglish.bsky.social · Apr 8

Grab serum from virally infected (here, COVID) patients to map and monitor single molecule quasi-species distributions of the circulating genomes (would suggest deeper than MinIon reads, we repeat sample preparation multiple times. GridIon probably best).

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Justin English @justingenglish.bsky.social · Apr 8

Accurately quantify edit distributions from CRISPR/Cas9 genome KO pools.

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Justin English @justingenglish.bsky.social · Apr 8

So what can you do with something like this?

QC your viral preps to detect random-break packaging issues not observable in Illumina sequencing.

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Justin English @justingenglish.bsky.social · Apr 8

We develop:
1. Bootstrap algorithm to benchmark # of clusters needed to give accurate sequences on a per run basis.
2. Our own aligner to overcome tandem repeat issues
3. A Docker-based GUI wrapper for the program.

Get it here:
github.com/JGEnglishLab...

GitHub - JGEnglishLab/ConSeqUMI: Bioinformatics software package for increasing the accuracy of nanopore sequencing data.

Bioinformatics software package for increasing the accuracy of nanopore sequencing data. - JGEnglishLab/ConSeqUMI

github.com

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Justin English @justingenglish.bsky.social · Apr 8

Issue #3, Origin of Mismatches. We see rare mutations in our sequences. Are they real? Yes, we develop a method to PCR the samples directly and confirm by Sanger. Where are they from, bacterial passaging or PCR? Ran LTE of bacteria and repeated PCR -- both contribute, PCR orders of magnitude more.

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Justin English @justingenglish.bsky.social · Apr 8

Issue #2, Abundance Reproducibility. Is the content of a sample accurately reproduced in the data output? We mixed plasmids of known sequence together in a logarithmic range of concentrations and repeatedly measured the sample demonstrating reproducible, accurate readout of abundances.

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Justin English @justingenglish.bsky.social · Apr 8

Issue #1, Chimeric Molecules. Inevitable oligo contamination between tagging and amplification rounds creates hybrid pairs. How to accurately discard them computationally? Using a deep barcoded template as an internal barcode we observed chimera formation patterns and programmed to filter them out.

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Justin English @justingenglish.bsky.social · Apr 8

This work was led by Adam Zahm and Caleb Cranney in our group. There are lots of unique molecular index (UMI) strategies out there, but both the software packages and ground-truth sequence accuracy validations were severely lacking. So we decided to tackle this problem and deliver a unified solution

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Justin English @justingenglish.bsky.social · Apr 8

Want to Nanopore sequence complex nucleotide populations accurately, at low cost, with QC standards, using a plug-and-play informatics GUI, where you can PCR observed sequences out from your sample and not synthesize them? See our new pre-print!

www.biorxiv.org/content/10.1...

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McSweeney's @mcsweeneys.net · Apr 6

"Within a week, I was already experiencing the benefits of intermittent working. My bloodshot eyes faded from red to dark pink, and my back hunch started to unfurl. I found myself forming new thoughts that had nothing to do with performing wage labor."

I’m Trying a Wild Experimental Diet Where I Restrict My Working Hours to Certain Times of the Day

I never thought I’d follow a dieting fad. I always prided myself on being the type of laid-back person who worked as much as I wanted, whenever I w...

www.mcsweeneys.net

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Eric Topol @erictopol.bsky.social · Apr 4

More from Peter Marks on RFK Jr and the FDA
This extends beyond anti-vax to unproven use of stem cells
Gift link
www.wsj.com/health/healt...

Exclusive | Ousted Vaccine Chief Says RFK Jr.’s Team Sought Data to Justify Anti-Science Stance

Peter Marks says the new health secretary’s team wants to show vaccines aren’t safe while promoting dangerous and unproven treatments.

www.wsj.com

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Karin Wulf @kawulf.bsky.social · Apr 2

"It has come for science because it was never just about the Humanities, but about how we assess American progress through infrastructures of new knowledge and its application." scholarlykitchen.sspnet.org/2025/04/02/t...

The Humanities as Canary: Understanding this Crisis Now - The Scholarly Kitchen

The Humanities have always been the canary in the coal mine of the full knowledge industry. What information can help us understand this crisis and its implications?

scholarlykitchen.sspnet.org

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Justin English @justingenglish.bsky.social · Apr 4

GPCR allosterism, a popular #ASPET2025 session chaired by @laurenslosky.bsky.social & Laura Wingler.

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WIRED @wired.com · Mar 25

Signal is a great privacy tool, but it isn’t magic. And even if you’re not discussing war plans in your group chat, it’s a good idea to know the limits of encryption.

Read our piece on what Signal can—and can’t—do for you here: www.wired.com/story/encryp...

Encrypted Messaging Is Essential—But It Isn’t Magic

As recent events have shown, using an encrypted messaging app like WhatsApp or Signal is no privacy panacea.

www.wired.com

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Journal of Cell Biology @jcb.org · Mar 25

Review: Ripoll, von Zastrow and @emilyblythe.bsky.social discuss the evolving understanding of cellular #GPCR signaling, highlighting recent advances and noting caveats and open questions. rupress.org/jcb/article/...

#CellSignaling #Physiology

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Eric Leonardis @ericleonardis.bsky.social · Mar 25

That’s right, I’m the worst kind of super villain in this country… I’m a *checks notes* NIH trainee 😂

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Justin English @justingenglish.bsky.social · Mar 25

so you're saying American financial policy decisions should be made to appease and court our least responsible voters? Or that we should pump and dump them like our current President and make them poorer?

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Mark Harris @markharris.bsky.social · Mar 25

The job of Democrats is so clear right now: It's to do everything possible in the next 48 hours to keep the Atlantic story front-burner and make people understand the issues and the stakes. It couldn't be a simpler test of who gets it and who doesn't.

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Daniel Gorelick @danielgorelick.bsky.social · Mar 25

New preprint, very proud of this one www.biorxiv.org/content/10.1...

Fast & Fair peer review: a pilot study demonstrating feasibility of rapid, high-quality peer review in a biology journal

Traditional peer review is slow, often delayed by the time-consuming process of identifying reviewers and lengthy review turnaround times. This study tests the feasibility of the Fast & Fair peer revi...

www.biorxiv.org

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Justin English @justingenglish.bsky.social · Mar 25

"GOP warms to idea children should live" just to keep it wholesome.

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